utils: Import data from polymapR

Description Usage Arguments Details Value Author(s) References

Description

Function to import datasets from polymapR. Function from MAPpoly.

This function converts linkage phase configurations from matrix form to list

Computes the polysomic segregation frequency given a ploidy level and the dosage of the locus in both parents. It does not consider double reduction.

Function to import phased map lists from polymapR. Function from MAPpoly.

This function converts linkage phase configurations from list to matrix form

Usage

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import_data_from_polymapR(
  input.data,
  ploidy,
  parent1 = "P1",
  parent2 = "P2",
  input.type = c("discrete", "probabilistic"),
  prob.thres = 0.95,
  pardose = NULL,
  offspring = NULL,
  filter.non.conforming = TRUE,
  verbose = TRUE
)

filter_non_conforming_classes(input.data, prob.thres = NULL)

ph_matrix_to_list(M)

is.prob.data(x)

mf_h(d)

mrk_chisq_test(x, ploidy)

dist_prob_to_class(geno, prob.thres = 0.9)

segreg_poly(ploidy, d.p1, d.p2)

import_phased_maplist_from_polymapR(maplist, mappoly.data, ploidy = NULL)

prepare_map(input.map, config = "best")

imf_h(r)

get_LOD(x, sorted = TRUE)

ph_list_to_matrix(L, ploidy)

Arguments

input.data

a polymapR dataset

ploidy

ploidy level

parent1

a character string containing the name (or pattern of genotype IDs) of parent 1

parent2

a character string containing the name (or pattern of genotype IDs) of parent 2

input.type

Indicates whether the input is discrete ("disc") or probabilistic ("prob")

prob.thres

probability threshold to select the genotype. Values below this genotype are assumed as missing data

pardose

matrix of dimensions (n.mrk x 3) containing the name of the markers in the first column, and the dosage of parents 1 and 2 in columns 2 and 3. (see polymapR vignette)

offspring

a character string containing the name (or pattern of genotype IDs) of the offspring individuals. If NULL (default) it considers all individuals as offsprings, except parent1 and parent2.

filter.non.conforming

if TRUE exclude samples with non expected genotypes under no double reduction. Since markers were already filtered in polymapR, the default is FALSE.

verbose

if TRUE (default), the current progress is shown; if FALSE, no output is produced

M

matrix whose columns represent homologous chromosomes and the rows represent markers

x

an object of class mappoly.map

geno

the probabilistic genotypes contained in the object 'mappoly.data'

d.p1

the dosage in parent P

d.p2

the dosage in parent Q

maplist

a list of phased maps obtained using function create_phased_maplist from package polymapR

mappoly.data

a dataset used to obtain maplist, converted into class mappoly.data

sorted

logical. if TRUE, the LOD Scores are displayed in a decreasing order

L

a list of configuration phases

void

internal function to be documented

Details

See examples at https://rpubs.com/mmollin/tetra_mappoly_vignette.

See examples at https://rpubs.com/mmollin/tetra_mappoly_vignette.

Value

a list of linkage phase configurations

a matrix containing the doses of each genotype and marker. Markers are disposed in rows and individuals are disposed in columns. Missing data are represented by NAs

a vector containing the expected segregation frequency for all possible genotypic classes.

a numeric vector containing the LOD Scores

a matrix whose columns represent homologous chromosomes and the rows represent markers

Author(s)

Marcelo Mollinari mmollin@ncsu.edu

Marcelo Mollinari, mmollin@ncsu.edu

Marcelo Mollinari mmollin@ncsu.edu

References

Bourke PM et al: (2019) PolymapR — linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496–3502. doi: 10.1093/bioinformatics/bty1002

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Serang O, Mollinari M, Garcia AAF (2012) Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids. _PLoS ONE_ 7(2): e30906.

Bourke PM et al: (2019) PolymapR — linkage analysis and genetic map construction from F1 populations of outcrossing polyploids. _Bioinformatics_ 34:3496–3502. doi: 10.1093/bioinformatics/bty1002

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378


viewpoly documentation built on Jan. 3, 2022, 5:10 p.m.